while building rdkit some ctest failed

[Rumeza]

95% tests passed, 10 tests failed out of 212

Total Test time (real) = 8449.33 sec

The following tests FAILED:
52 - pyDepictor (Failed)
80 - pyChemReactions (Failed)
116 - pyTestGenerator (Failed)
117 - pyTestMHFP (Failed)
129 - pyDistGeomHelpers (Failed)
148 - pyMolHash (Failed)
168 - pyMolInterchange (Failed)
171 - pyGraphMolWrap (Timeout)
206 - pythonTestDirML (Failed)
212 - pythonTestDirChem (Timeout)
Can you help me in resolving these failures.

Start 52: pyDepictor

52: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py"
52: Test timeout computed to be: 1500
52: Traceback (most recent call last):
52: File "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 113, in
52: class TestCase(unittest.TestCase):
52: File "/home/farah/rdkit/Code/GraphMol/Depictor/Wrap/testDepictor.py", line 536, in TestCase
52: @unittest.skipIf(not rdDepictor.IsCoordGenSupportAvailable(), "CoordGen not available, skipping")
52: AttributeError: module 'rdkit.Chem.rdDepictor' has no attribute 'IsCoordGenSupportAvailable'
1/1 Test facebook/mvfst#52: pyDepictor .......................***Failed 3.57 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 3.76 sec

The following tests FAILED:
52 - pyDepictor (Failed)

@Rumeza
Author
Rumeza commented 2 hours ago
Start 80: pyChemReactions

80: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py"
80: Test timeout computed to be: 1500
80: [19:17:03]
80:
80: ****
80: Pre-condition Violation
80: getNumImplicitHs() called without preceding call to calcImplicitValence()
80: Violation occurred on line 297 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp
80: Failed Expression: d_implicitValence > -1
80: ****
80:
80: [19:17:03]
80:
80: ****
80: Pre-condition Violation
80: getNumImplicitHs() called without preceding call to calcImplicitValence()
80: Violation occurred on line 297 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp
80: Failed Expression: d_implicitValence > -1
80: ****
80:
80: ...[19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
80: [19:17:03] stereo atoms in input cannot be mapped to output (atoms are no longer bonded)
80: .[19:17:03] product atom-mapping number 1 found multiple times.
80: FFF.F...F.......[19:17:03] mapped atoms in the reactants were not mapped in the products.
80: unmapped numbers are: 3
80: [19:17:03] mapped atoms in the reactants were not mapped in the products.
80: unmapped numbers are: 3
80: .[19:17:03] mapped atoms in the reactants were not mapped in the products.
80: unmapped numbers are: 3
80: ../home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:515: DeprecationWarning: Please use assertTrue instead.
80: self.failUnless(rxn)
80: [19:17:03] reactant 2 has no mapped atoms.
80: [19:17:03] reactant 2 has no mapped atoms.
80: [19:17:03] product 1 has no mapped atoms.
80: ../home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:558: DeprecationWarning: Please use assertEqual instead.
80: self.assertEquals(res, res2)
80: ......[19:17:03] SMARTS Parse Error: syntax error while parsing: C:1Q
80: [19:17:03] SMARTS Parse Error: Failed parsing SMARTS 'C:1Q' for input: 'C:1Q'
80: [19:17:03] SMARTS Parse Error: syntax error while parsing: C:1[N:3]Q
80: [19:17:03] SMARTS Parse Error: Failed parsing SMARTS 'C:1[N:3]Q' for input: 'C:1[N:3]Q'
80: .[19:17:03] reactant atom-mapping number 1 found multiple times.
80: [19:17:03] product atom-mapping number 2 not found in reactants.
80: [19:17:03] mapped atoms in the reactants were not mapped in the products.
80: unmapped numbers are: 4
80: [19:17:03] product atom-mapping number 5 not found in reactants.
80: ........./home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:739: DeprecationWarning: Please use assertFalse instead.
80: self.failIf(rxn is None)
80: /home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py:745: ResourceWarning: unclosed file <_io.BufferedReader name='/home/farah/rdkit/Code/GraphMol/ChemReactions/testData/reaction1.no_metadata.png'>
80: png = open(fname, 'rb').read()
80: ResourceWarning: Enable tracemalloc to get the object allocation traceback
80: ..[19:17:04] SMARTS Parse Error: syntax error while parsing: boromicacid
80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
80: [19:17:04] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
80: [19:17:04] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
80: [19:17:04] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
80: [19:17:04] reaction has no reactants
80: [19:17:04] reaction has no products
80: [19:17:04] initialization failed
80: [19:17:04] reaction has no reactants
80: [19:17:04] reaction has no products
80: .[19:17:04] SMARTS Parse Error: syntax error while parsing: boromicacid
80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'boromicacid' for input: 'boromicacid'
80: [19:17:05] SMARTS Parse Error: syntax error while parsing: carboxylicacid,acidchlroide
80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxylicacid,acidchlroide' for input: 'carboxylicacid,acidchlroide'
80: [19:17:05] SMARTS Parse Error: syntax error while parsing: carboxyliccaid,acidchloride
80: [19:17:05] SMARTS Parse Error: Failed parsing SMARTS 'carboxyliccaid,acidchloride' for input: 'carboxyliccaid,acidchloride'
80: [19:17:05] reaction has no reactants
80: [19:17:05] reaction has no products
80: [19:17:05] initialization failed
80: [19:17:05] reaction has no reactants
80: [19:17:05] reaction has no products
80: .
80: ======================================================================
80: FAIL: test_reaction_copies_stereogroup (main.StereoGroupTests)
80: If multiple copies of an atom in StereoGroup show up in the product, they
80: ----------------------------------------------------------------------
80: Traceback (most recent call last):
80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 938, in test_reaction_copies_stereogroup
80: self.assertEqual(
80: AssertionError: 'CC(C)(OCCC@@HCC@@HBr)OCCC@@HCC@@HBr |&1:6,9,15,18|' != 'CC(C)(OCCC@HCC@HBr)OCCC@HCC@HBr |&1:6,9,15,18|'
80: - CC(C)(OCCC@@HCC@@HBr)OCCC@@HCC@@HBr |&1:6,9,15,18|
80: ? - - - -
80: + CC(C)(OCCC@HCC@HBr)OCCC@HCC@HBr |&1:6,9,15,18|
80:
80:
80: ======================================================================
80: FAIL: test_reaction_defines_stereo (main.StereoGroupTests)
80: StereoGroup atoms are in the reaction, and the reaction creates the specified
80: ----------------------------------------------------------------------
80: Traceback (most recent call last):
80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 892, in test_reaction_defines_stereo
80: self.assertEqual(products, 'FC@@HC@HBr |&1:3|')
80: AssertionError: 'FC@@HC@@HBr |&1:3|' != 'FC@@HC@HBr |&1:3|'
80: - FC@@HC@@HBr |&1:3|
80: ? -
80: + FC@@HC@HBr |&1:3|
80:
80:
80: ======================================================================
80: FAIL: test_reaction_destroys_stereo (main.StereoGroupTests)
80: StereoGroup atoms are in the reaction, and the reaction destroys the specified
80: ----------------------------------------------------------------------
80: Traceback (most recent call last):
80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 871, in test_reaction_destroys_stereo
80: self.assertEqual(products, 'FC(Cl)C@HBr |&1:3|')
80: AssertionError: 'FC(Cl)C@@HBr |&1:3|' != 'FC(Cl)C@HBr |&1:3|'
80: - FC(Cl)C@@HBr |&1:3|
80: ? -
80: + FC(Cl)C@HBr |&1:3|
80:
80:
80: ======================================================================
80: FAIL: test_reaction_inverts_stereo (main.StereoGroupTests)
80: StereoGroup atoms are in the reaction, and the reaction inverts the specified
80: ----------------------------------------------------------------------
80: Traceback (most recent call last):
80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 848, in test_reaction_inverts_stereo
80: self.assertEqual(products, 'FC@HBr |o1:1|')
80: AssertionError: 'FC@@HBr |o1:1|' != 'FC@HBr |o1:1|'
80: - FC@@HBr |o1:1|
80: ? -
80: + FC@HBr |o1:1|
80:
80:
80: ======================================================================
80: FAIL: test_stereogroup_is_spectator_to_reaction (main.StereoGroupTests)
80: StereoGroup atoms are not in the reaction
80: ----------------------------------------------------------------------
80: Traceback (most recent call last):
80: File "/home/farah/rdkit/Code/GraphMol/ChemReactions/Wrap/testReactionWrapper.py", line 905, in test_stereogroup_is_spectator_to_reaction
80: self.assertEqual(products, 'FC@HC@HBr |o1:3|')
80: AssertionError: 'FC@HC@@HBr |o1:3|' != 'FC@HC@HBr |o1:3|'
80: - FC@HC@@HBr |o1:3|
80: ? -
80: + FC@HC@HBr |o1:3|

Start 116: pyTestGenerator

116: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py"
116: Test timeout computed to be: 1500
116: F...E.E....E
116: ======================================================================
116: ERROR: testFingerprintOptions (main.TestCase)
116: ----------------------------------------------------------------------
116: Traceback (most recent call last):
116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 304, in testFingerprintOptions
116: g.GetOptions().numBitsPerFeature = 2
116: AttributeError: 'FingerprintGenerator64' object has no attribute 'GetOptions'
116:
116: ======================================================================
116: ERROR: testMorganRedundantEnvironments (main.TestCase)
116: ----------------------------------------------------------------------
116: Traceback (most recent call last):
116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 293, in testMorganRedundantEnvironments
116: g = rdFingerprintGenerator.GetMorganGenerator(2, includeRedundantEnvironments=True)
116: Boost.Python.ArgumentError: Python argument types in
116: rdkit.Chem.rdFingerprintGenerator.GetMorganGenerator(int)
116: did not match C++ signature:
116: GetMorganGenerator(unsigned int radius=3, bool countSimulation=False, bool includeChirality=False, bool useBondTypes=True, bool onlyNonzeroInvariants=False, bool includeRingMembership=True, boost::python::api::object {lvalue} countBounds=None, unsigned int fpSize=2048, boost::python::api::object {lvalue} atomInvariantsGenerator=None, boost::python::api::object {lvalue} bondInvariantsGenerator=None)
116:
116: ======================================================================
116: ERROR: testTopologicalTorsionShortestPaths (main.TestCase)
116: ----------------------------------------------------------------------
116: Traceback (most recent call last):
116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 338, in testTopologicalTorsionShortestPaths
116: g.GetOptions().onlyShortestPaths = True
116: AttributeError: 'FingerprintGenerator64' object has no attribute 'GetOptions'
116:
116: ======================================================================
116: FAIL: testAdditionalOutput (main.TestCase)
116: ----------------------------------------------------------------------
116: Traceback (most recent call last):
116: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testGenerators.py", line 231, in testAdditionalOutput
116: self.assertEqual(ao.GetAtomToBits(), ((1404, 1916), (1404, 1596), (1596, 1916)))
116: AssertionError: Tuples differ: ((351, 479), (351, 399), (479, 399)) != ((1404, 1916), (1404, 1596), (1596, 1916))
116:
116: First differing element 0:
116: (351, 479)
116: (1404, 1916)
116:
116: - ((351, 479), (351, 399), (479, 399))
116: + ((1404, 1916), (1404, 1596), (1596, 1916))
116:
116: ----------------------------------------------------------------------
116: Ran 12 tests in 0.637s
116:
116: FAILED (failures=1, errors=3)
1/1 Test facebook/mvfst#116: pyTestGenerator ..................***Failed 4.16 sec

Start 117: pyTestMHFP

117: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py"
117: Test timeout computed to be: 1500
117: FF
117: ======================================================================
117: FAIL: testMHFPDistance (main.TestCase)
117: ----------------------------------------------------------------------
117: Traceback (most recent call last):
117: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py", line 25, in testMHFPDistance
117: self.assertEqual(dist, 0.0)
117: AssertionError: 1.0 != 0.0
117:
117: ======================================================================
117: FAIL: testMHFPFingerprint (main.TestCase)
117: ----------------------------------------------------------------------
117: Traceback (most recent call last):
117: File "/home/farah/rdkit/Code/GraphMol/Fingerprints/Wrap/testMHFP.py", line 50, in testMHFPFingerprint
117: self.assertEqual(dist, 0.5390625)
117: AssertionError: 0.4609375 != 0.5390625
117:
117: ----------------------------------------------------------------------
117: Ran 2 tests in 0.388s
117:
117: FAILED (failures=2)
1/1 Test facebook/mvfst#117: pyTestMHFP .......................***Failed 2.97 sec

Start 129: pyDistGeomHelpers

129: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/DistGeomHelpers/Wrap/testDistGeom.py"
129: Test timeout computed to be: 1500
129: .[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: ..[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: ..[19:36:52] Molecule does not have explicit Hs. Consider calling AddHs()
129: .[19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:53] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:54] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:55] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:56] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:57] Molecule does not have explicit Hs. Consider calling AddHs()
129: .[19:36:57] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:36:58] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:00] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:01] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:03] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:05] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:12] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:13] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:15] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:16] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:20] Molecule does not have explicit Hs. Consider calling AddHs()
129: [19:37:22] Molecule does not have explicit Hs. Consider calling AddHs()
129: .[19:37:31] Molecule does not have explicit Hs. Consider calling AddHs()

Start 148: pyMolHash

148: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/MolHash/Wrap/testMolHash.py"
148: Test timeout computed to be: 1500
148: .F
148: ======================================================================
148: FAIL: testCxSmiles (main.TestCase)
148: ----------------------------------------------------------------------
148: Traceback (most recent call last):
148: File "/home/farah/rdkit/Code/GraphMol/MolHash/Wrap/testMolHash.py", line 42, in testCxSmiles
148: self.assertEqual(rdMolHash.MolHash(m, rdMolHash.HashFunction.HetAtomTautomer),
148: AssertionError: 'CC@HC@@HCC([C]1[CH][N][CH][N]1)[C]1[CH][N][CH][N]1_3_0' != 'CC@HC@@HC@H[O]_3_0'
148: - CC@HC@@HCC([C]1[CH][N][CH][N]1)[C]1[CH][N][CH][N]1_3_0
148: + CC@HC@@HC@H[O]_3_0
148:
148:
148: ----------------------------------------------------------------------
148: Ran 2 tests in 0.183s
148:
148: FAILED (failures=1)
1/1 Test facebook/mvfst#148: pyMolHash ........................***Failed 2.65 sec

Start 168: pyMolInterchange

168: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py"
168: Test timeout computed to be: 1500
168: .F
168: ======================================================================
168: FAIL: test2 (main.TestCase)
168: ----------------------------------------------------------------------
168: Traceback (most recent call last):
168: File "/home/farah/rdkit/Code/GraphMol/MolInterchange/Wrap/testMolInterchange.py", line 33, in test2
168: self.assertIn('stereoGroups',json)
168: AssertionError: 'stereoGroups' not found in '{"commonchem":{"version":10},"defaults":{"atom":{"z":6,"impHs":0,"chg":0,"nRad":0,"isotope":0,"stereo":"unspecified"},"bond":{"bo":1,"stereo":"unspecified"}},"molecules":[{"atoms":[{"impHs":3},{"impHs":1,"stereo":"ccw"},{"z":8,"impHs":1},{"impHs":2},{"impHs":1,"stereo":"cw"},{"impHs":3},{"z":9}],"bonds":[{"atoms":[0,1]},{"atoms":[1,2]},{"atoms":[1,3]},{"atoms":[3,4]},{"atoms":[4,5]},{"atoms":[4,6]}],"extensions":[{"name":"rdkitRepresentation","formatVersion":2,"toolkitVersion":"2022.09.4","cipRanks":[0,3,5,2,4,1,6],"cipCodes":[[1,"S"],[4,"R"]]}]}]}'
168:
168: ----------------------------------------------------------------------
168: Ran 2 tests in 0.263s
168:
168: FAILED (failures=1)
1/1 Test facebook/mvfst#168: pyMolInterchange .................***Failed 3.70 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 3.90 sec

The following tests FAILED:
168 - pyMolInterchange (Failed)

Start 171: pyGraphMolWrap

171: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/Code/GraphMol/Wrap/rough_test.py"
171: Test timeout computed to be: 1500
171: ..............[19:50:54] SMARTS Parse Error: syntax error while parsing: fiib
171: [19:50:54] SMARTS Parse Error: Failed parsing SMARTS 'fiib' for input: 'fiib'
171: ....[19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] Spurious data before the first property will be ignored
171: [19:50:54] Property will be truncated after the first blank line
171: [19:50:54] Property will be truncated after the first blank line
171: [19:50:54] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
171: [19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] Spurious data before the first property will be ignored
171: [19:50:54] Property will be truncated after the first blank line
171: [19:50:54] Property will be truncated after the first blank line
171: [19:50:54] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
171: [19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
171: [19:50:54] ERROR: Problems encountered parsing data fields
171: [19:50:54] ERROR: moving to the beginning of the next molecule
171: [19:50:54] Property <ANOTHER_PROPERTY> will be truncated after the first blank line
171: .[19:50:54] SMILES Parse Error: syntax error while parsing: fail
171: [19:50:54] SMILES Parse Error: Failed parsing SMILES 'fail' for input: 'fail'
171: [19:50:54] ERROR: Smiles parse error on line 2
171: [19:50:54] ERROR: Cannot create molecule from : 'fail'
171: >>> This may result in an infinite loop. It should finish almost instantly
171: <<< OK, it finished.
171: ............[19:50:55] Explicit valence for atom # 1 C, 5, is greater than permitted
171: ........../home/farah/rdkit/Code/GraphMol/Wrap/rough_test.py:2155: DeprecationWarning: Please use assertEqual instead.
171: self.assertEquals(ri.AtomRingFamilies(), ())
171: ..[19:50:55] non-ring atom 0 marked aromatic
171: [19:50:55] non-ring atom 0 marked aromatic
171: [19:50:55]
171:
171: ****
171: Range Error
171: idx
171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp
171: Failed Expression: 12 < 6
171: ****
171:
171: [19:50:55] non-ring atom 0 marked aromatic
171: [19:50:55] non-ring atom 0 marked aromatic
171: [19:50:55]
171:
171: ****
171: Range Error
171: idx
171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp
171: Failed Expression: 12 < 6
171: ****
171:
171: ...............[19:50:56] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count.
171: [19:50:56] WARNING: the onlyHeavy argument to mol.GetNumAtoms() has been deprecated. Please use the onlyExplicit argument instead or mol.GetNumHeavyAtoms() if you want the heavy atom count.
171: ..............[19:50:56] Can't kekulize mol. Unkekulized atoms: 0 1 2 3 4
171: [19:50:56] Explicit valence for atom # 1 C, 5, is greater than permitted
171: ...........................[19:51:44] unable to set wavy bonds for double bonds: 3
171: .........[19:51:44]
171:
171: ****
171: Range Error
171: idx
171: Violation occurred on line 213 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/ROMol.cpp
171: Failed Expression: 6 < 5
171: ****
171:
171: ...................[19:52:02] Explicit valence for atom # 1 F, 2, is greater than permitted
171: [19:52:02] Explicit valence for atom # 6 F, 2, is greater than permitted
171: [19:52:02] Can't kekulize mol. Unkekulized atoms: 3 4 5
171: .[19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero
171: [19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero
171: [19:52:02] Warning: molecule is tagged as 3D, but all Z coords are zero
171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero
171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero
171: [19:52:03] Warning: molecule is tagged as 3D, but all Z coords are zero
171: ...............[19:52:35]
171:
171: ****
171: Pre-condition Violation
171: no owner
171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h
171: Failed Expression: dp_mol
171: ****
171:
171: [19:52:35]
171:
171: ****
171: Pre-condition Violation
171: no owner
171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h
171: Failed Expression: dp_mol
171: ****
171:
171: [19:52:35]
171:
171: ****
171: Pre-condition Violation
171: no owner
171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h
171: Failed Expression: dp_mol
171: ****
171:
171: [19:52:35]
171:
171: ****
171: Pre-condition Violation
171: no owner
171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h
171: Failed Expression: dp_mol
171: ****
171:
171: [19:52:35]
171:
171: ****
171: Pre-condition Violation
171: no owner
171: Violation occurred on line 138 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.h
171: Failed Expression: dp_mol
171: ****
171:
171: .....[19:52:35]
171:
171: ****
171: Range Error
171: atomIdx1
171: Violation occurred on line 331 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/RWMol.cpp
171: Failed Expression: 0 < 0
171: ****
171:
171: ......[19:52:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
171: [19:52:35] ERROR: Smiles parse error on line 0
171: [19:52:35] ERROR: Cannot create molecule from : 'c1ccccc'
171: [19:52:35] SMILES Parse Error: extra open parentheses for input: 'C(C'
171: [19:52:35] ERROR: Smiles parse error on line 3
171: [19:52:35] ERROR: Cannot create molecule from : 'C(C'
171: [19:52:35] Explicit valence for atom # 1 C, 5, is greater than permitted
171: [19:52:35] ERROR: Could not sanitize molecule on line 6
171: [19:52:35] ERROR: Explicit valence for atom # 1 C, 5, is greater than permitted
171: [19:52:35] SMILES Parse Error: unclosed ring for input: 'c1ccccc'
171: [19:52:35] ERROR: Smiles parse error on line 0
171: [19:52:35] ERROR: Cannot create molecule from : 'c1ccccc'
171: [19:52:35] SMILES Parse Error: extra open parentheses for input: 'C(C'
171: [19:52:35] ERROR: Smiles parse error on line 3
171: [19:52:35] ERROR: Cannot create molecule from : 'C(C'
171: [19:52:35] SMILES Parse Error: unclosed ring for input: 'C1C(Cl)CCCC'
171: [19:52:35] ERROR: Smiles parse error on line 6
171: [19:52:35] ERROR: Cannot create molecule from : 'C1C(Cl)CCCC'
171: [19:52:35] Explicit valence for atom # 1 F, 2, is greater than permitted
171: [19:52:35] ERROR: Could not sanitize molecule ending on line 21
171: [19:52:35] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
171: [19:52:35] ERROR: EOF hit while reading atoms
171: [19:52:35] ERROR: moving to the beginning of the next molecule
171: [19:52:35] Explicit valence for atom # 1 F, 2, is greater than permitted
171: [19:52:35] ERROR: Could not sanitize molecule ending on line 21
171: [19:52:35] ERROR: Explicit valence for atom # 1 F, 2, is greater than permitted
171: [19:52:35] ERROR: EOF hit while reading atoms
171: [19:52:35] ERROR: moving to the beginning of the next molecule
171: ....[19:52:36]
171:
171: ****
171: Pre-condition Violation
171: RingInfo not initialized
171: Violation occurred on line 169 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/RingInfo.cpp
171: Failed Expression: df_init
171: ****
1/1 Test facebook/mvfst#171: pyGraphMolWrap ...................***Timeout 1500.18 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 1500.39 sec

Start 206: pythonTestDirML

206: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/rdkit/ML/test_list.py" "--testDir" "/home/farah/rdkit/rdkit/ML"
206: Test timeout computed to be: 1500
206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/SplitData.py:124: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(perm, random=random.random)
206: .......
206: ----------------------------------------------------------------------
206: Ran 7 tests in 6.200s
206:
206: OK
206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/ScreenComposite.py:429: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
206: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
206: voteTab = numpy.zeros((nResultCodes, nResultCodes), numpy.int)
206: ./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/SplitData.py:124: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(perm, random=random.random)
206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:68: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(res, random=random.random)
206: ......../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:655: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(acts, random=random.random)
206: ...
206: ----------------------------------------------------------------------
206: Ran 12 tests in 1.039s
206:
206: OK
206: .
206: ----------------------------------------------------------------------
206: Ran 1 test in 0.385s
206:
206: OK
206: ...
206: ----------------------------------------------------------------------
206: Ran 3 tests in 0.018s
206:
206: OK
206: ........
206: ----------------------------------------------------------------------
206: Ran 8 tests in 0.015s
206:
206: OK
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 4.527s
206:
206: OK
206: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:68: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(res, random=random.random)
206: .....
206: ----------------------------------------------------------------------
206: Ran 5 tests in 0.022s
206:
206: OK
206: ......./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/Data/DataUtils.py:655: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(acts, random=random.random)
206: ..
206: ----------------------------------------------------------------------
206: Ran 9 tests in 0.033s
206:
206: OK
206: ............
206: ----------------------------------------------------------------------
206: Ran 12 tests in 0.028s
206:
206: OK
206: .....
206: ----------------------------------------------------------------------
206: Ran 5 tests in 0.467s
206:
206: OK
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 208, in main.SplitDbData
206: Failed example:
206: train,test = SplitDbData(conn,1./3.,'basic_2class')
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[5]>", line 1, in
206: train,test = SplitDbData(conn,1./3.,'basic_2class')
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 261, in SplitDbData
206: train, test = SplitIndices(nRes, frac, silent=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 209, in main.SplitDbData
206: Failed example:
206: [str(x) for x in train]
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[6]>", line 1, in
206: [str(x) for x in train]
206: NameError: name 'train' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 214, in main.SplitDbData
206: Failed example:
206: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1)
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[8]>", line 1, in
206: train,test = SplitDbData(conn,.5,'basic_2class',useActs=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData
206: train, test = SplitIndices(nRes, frac, silent=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 215, in main.SplitDbData
206: Failed example:
206: [str(x) for x in train]
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[9]>", line 1, in
206: [str(x) for x in train]
206: NameError: name 'train' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 223, in main.SplitDbData
206: Failed example:
206: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1)
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[11]>", line 1, in
206: train,test = SplitDbData(conn,[.5,1./3.],'basic_2class',useActs=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData
206: train, test = SplitIndices(nRes, frac, silent=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 224, in main.SplitDbData
206: Failed example:
206: [str(x) for x in train]
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[12]>", line 1, in
206: [str(x) for x in train]
206: NameError: name 'train' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 230, in main.SplitDbData
206: Failed example:
206: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0])
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[14]>", line 1, in
206: train,test = SplitDbData(conn,.5,'float_2class',useActs=1,actBounds=[1.0])
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 289, in SplitDbData
206: train, test = SplitIndices(nRes, frac, silent=1)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 231, in main.SplitDbData
206: Failed example:
206: [str(x) for x in train]
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitDbData[15]>", line 1, in
206: [str(x) for x in train]
206: NameError: name 'train' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 54, in main.SplitIndices
206: Failed example:
206: test,train = SplitIndices(10,.5)
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[2]>", line 1, in
206: test,train = SplitIndices(10,.5)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 55, in main.SplitIndices
206: Failed example:
206: test
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[3]>", line 1, in
206: test
206: NameError: name 'test' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 57, in main.SplitIndices
206: Failed example:
206: train
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[4]>", line 1, in
206: train
206: NameError: name 'train' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 60, in main.SplitIndices
206: Failed example:
206: test,train = SplitIndices(10,.5)
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[5]>", line 1, in
206: test,train = SplitIndices(10,.5)
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 124, in SplitIndices
206: RDRandom.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 61, in main.SplitIndices
206: Failed example:
206: test
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[6]>", line 1, in
206: test
206: NameError: name 'test' is not defined
206: **********************************************************************
206: File "/home/farah/rdkit/rdkit/ML/Data/SplitData.py", line 63, in main.SplitIndices
206: Failed example:
206: train
206: Exception raised:
206: Traceback (most recent call last):
206: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
206: exec(compile(example.source, filename, "single",
206: File "<doctest main.SplitIndices[7]>", line 1, in
206: train
206: NameError: name 'train' is not defined
206: **********************************************************************
206: 2 items had failures:
206: 8 of 16 in main.SplitDbData
206: 6 of 22 in main.SplitIndices
206: Test Failed 14 failures.
206: !!! TEST FAILURE: python SplitData.py {}
206: .
206: ----------------------------------------------------------------------
206: Ran 1 test in 0.025s
206:
206: OK
206: ......
206: ----------------------------------------------------------------------
206: Ran 6 tests in 0.023s
206:
206: OK
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 10.162s
206:
206: OK
206: ......
206: ----------------------------------------------------------------------
206: Ran 6 tests in 0.180s
206:
206: OK
206: ..
206: ----------------------------------------------------------------------
206: Ran 2 tests in 1.432s
206:
206: OK
206: ......../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/ML/DecTree/BuildQuantTree.py:34: DeprecationWarning: The random parameter to shuffle() has been deprecated
206: since Python 3.9 and will be removed in a subsequent version.
206: random.shuffle(ids, random=random.random)
206: ..
206: ----------------------------------------------------------------------
206: Ran 10 tests in 0.133s
206:
206: OK
206: .....
206: ----------------------------------------------------------------------
206: Ran 5 tests in 0.913s
206:
206: OK
206: ..
206: ----------------------------------------------------------------------
206: Ran 2 tests in 0.035s
206:
206: OK
206: .....
206: ----------------------------------------------------------------------
206: Ran 5 tests in 0.096s
206:
206: OK
206: ...
206: ----------------------------------------------------------------------
206: Ran 3 tests in 0.089s
206:
206: OK
206: EEE
206: ======================================================================
206: ERROR: test0CorrMat (main.TestCase)
206: ----------------------------------------------------------------------
206: Traceback (most recent call last):
206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp
206: random.shuffle(obits, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206:
206: ======================================================================
206: ERROR: test1Cluster (main.TestCase)
206: ----------------------------------------------------------------------
206: Traceback (most recent call last):
206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp
206: random.shuffle(obits, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206:
206: ======================================================================
206: ERROR: test_getValLTM (main.TestCase)
206: ----------------------------------------------------------------------
206: Traceback (most recent call last):
206: File "/home/farah/rdkit/rdkit/ML/InfoTheory/UnitTestCorrMatGen.py", line 48, in setUp
206: random.shuffle(obits, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206:
206: ----------------------------------------------------------------------
206: Ran 3 tests in 0.007s
206:
206: FAILED (errors=3)
206: !!! TEST FAILURE: python UnitTestCorrMatGen.py {}
206: ......
206: ----------------------------------------------------------------------
206: Ran 6 tests in 4.945s
206:
206: OK
206: ...EE..
206: ======================================================================
206: ERROR: testPerm1 (main.TestCase)
206: ----------------------------------------------------------------------
206: Traceback (most recent call last):
206: File "/home/farah/rdkit/rdkit/ML/ModelPackage/UnitTestPackage.py", line 101, in testPerm1
206: random.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206:
206: ======================================================================
206: ERROR: testPerm2 (main.TestCase)
206: ----------------------------------------------------------------------
206: Traceback (most recent call last):
206: File "/home/farah/rdkit/rdkit/ML/ModelPackage/UnitTestPackage.py", line 117, in testPerm2
206: random.shuffle(perm, random=random.random)
206: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
206:
206: ----------------------------------------------------------------------
206: Ran 7 tests in 0.847s
206:
206: FAILED (errors=2)
206: !!! TEST FAILURE: python UnitTestPackage.py {}
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 0.117s
206:
206: OK
206: .....
206: ----------------------------------------------------------------------
206: Ran 5 tests in 32.179s
206:
206: OK
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 0.013s
206:
206: OK
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 0.007s
206:
206: OK
206: ....
206: ----------------------------------------------------------------------
206: Ran 4 tests in 0.049s
206:
206: OK
206: !!! TEST FAILURE: python test_list.py {'dir': 'Data'}
206: !!! TEST FAILURE: python test_list.py {'dir': 'InfoTheory'}
206: !!! TEST FAILURE: python test_list.py {'dir': 'ModelPackage'}
1/1 Test facebook/mvfst#206: pythonTestDirML ..................***Failed 141.58 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 141.89 sec

The following tests FAILED:
206 - pythonTestDirML (Failed)

[Rumeza]

Start 212: pythonTestDirChem

212: Test command: /home/farah/anaconda3/bin/python "/home/farah/rdkit/rdkit/Chem/test_list.py" "--testDir" "/home/farah/rdkit/rdkit/Chem" "--buildType" "Release"
212: Test timeout computed to be: 1500
212: .......
212: ----------------------------------------------------------------------
212: Ran 7 tests in 1.748s
212:
212: OK
212: ......
212: ----------------------------------------------------------------------
212: Ran 6 tests in 0.770s
212:
212: OK
212: ....[20:26:27]
212:
212: ****
212: Pre-condition Violation
212: valence not defined for atoms not associated with molecules
212: Violation occurred on line 423 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/Atom.cpp
212: Failed Expression: dp_mol
212: ****
212:
212: .
212: ----------------------------------------------------------------------
212: Ran 5 tests in 0.227s
212:
212: OK
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 0.230s
212:
212: OK
212: ..
212: ----------------------------------------------------------------------
212: Ran 2 tests in 0.166s
212:
212: OK
212: ......................
212: ----------------------------------------------------------------------
212: Ran 22 tests in 0.422s
212:
212: OK
212: .....s..........E......ss
212: ======================================================================
212: ERROR: testIpc (main.TestCase)
212: ----------------------------------------------------------------------
212: Traceback (most recent call last):
212: File "/home/farah/rdkit/rdkit/Chem/UnitTestGraphDescriptors_2.py", line 117, in testIpc
212: avgIpc = GraphDescriptors.AvgIpc(m, forceDMat=1)
212: AttributeError: module 'rdkit.Chem.GraphDescriptors' has no attribute 'AvgIpc'
212:
212: ----------------------------------------------------------------------
212: Ran 25 tests in 1.884s
212:
212: FAILED (errors=1, skipped=3)
212: ..s
212: ----------------------------------------------------------------------
212: Ran 3 tests in 2.072s
212:
212: OK (skipped=1)
212: ...................................
212: ----------------------------------------------------------------------
212: Ran 35 tests in 1.462s
212:
212: OK
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 0.543s
212:
212: OK
212: .
212: ----------------------------------------------------------------------
212: Ran 1 test in 0.401s
212:
212: OK
212: .......
212: ----------------------------------------------------------------------
212: Ran 7 tests in 1.113s
212:
212: OK
212: ...
212: ----------------------------------------------------------------------
212: Ran 3 tests in 1.323s
212:
212: OK
212: .ss.ss.......
212: ----------------------------------------------------------------------
212: Ran 13 tests in 24.496s
212:
212: OK (skipped=4)
212: [20:27:51] Molecule does not have explicit Hs. Consider calling AddHs()
212: .[20:27:52] Molecule does not have explicit Hs. Consider calling AddHs()
212: ..............F....[20:37:28] WARNING: More than one matching pattern found - picking one
212:
212: [20:37:29] WARNING: More than one matching pattern found - picking one
212:
212: .[20:37:29] WARNING: More than one matching pattern found - picking one
212:
212: ...
212: ======================================================================
212: FAIL: testGithub6045 (main.TestCase)
212: ----------------------------------------------------------------------
212: Traceback (most recent call last):
212: File "/home/farah/rdkit/rdkit/Chem/UnitTestMol3D.py", line 471, in testGithub6045
212: self.assertEqual(len(prod.GetStereoGroups()), 0)
212: AssertionError: 1 != 0
212:
212: ----------------------------------------------------------------------
212: Ran 24 tests in 617.382s
212:
212: FAILED (failures=1)
212: {'C/C(F)=C/C@@HCl', 'C/C(F)=C/C@HCl', 'C/C(F)=C[C@@h](https://github.com/facebookincubator/mvfst/issues/C)Cl', 'C/C(F)=C[C@H](https://github.com/facebookincubator/mvfst/issues/C)Cl'}
212: {'C/C(F)=C/C@@HCl', 'C/C(F)=C/C@HCl', 'C/C(F)=C[C@@h](https://github.com/facebookincubator/mvfst/issues/C)Cl', 'C/C(F)=C[C@H](https://github.com/facebookincubator/mvfst/issues/C)Cl'}
212: {'FC@HC@@HCl', 'FC@@HC@@HCl', 'FC@HC@HCl'}
212: !!!! ['CC@HC@@HF', 'CC@@HC@@HBr', 'CC@@HC@@HF', 'CC@HC@@HBr', 'CC@@HC@HBr', 'CC@@HC@@HBr', 'CC@HC@HBr', 'CC@HC@@HBr']
212: ...../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BuildFragmentCatalog.py:164: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
212: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
212: resTbl = numpy.zeros((nBits, 2, nActs), numpy.int)
212: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BuildFragmentCatalog.py:228: DeprecationWarning: np.int is a deprecated alias for the builtin int. To silence this warning, use int by itself. Doing this will not modify any behavior and is safe. When replacing np.int, you may wish to use e.g. np.int64 or np.int32 to specify the precision. If you wish to review your current use, check the release note link for additional information.
212: Deprecated in NumPy 1.20; for more details and guidance: https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations
212: resTbl = numpy.zeros((nBits, 2, nActs), numpy.int)
212: ...
212: ----------------------------------------------------------------------
212: Ran 8 tests in 1.551s
212:
212: OK
212: .E...[20:38:49] WARNING: not removing hydrogen atom without neighbors
212: [20:38:50] WARNING: not removing hydrogen atom without neighbors
212: [20:38:50] WARNING: not removing hydrogen atom without neighbors
212: ....[20:38:50] WARNING: not removing hydrogen atom without neighbors
212: ......
212: ======================================================================
212: ERROR: testGetMolDescriptors (main.TestCase)
212: ----------------------------------------------------------------------
212: Traceback (most recent call last):
212: File "/home/farah/rdkit/rdkit/Chem/UnitTestDescriptors.py", line 204, in testGetMolDescriptors
212: descs = Descriptors.CalcMolDescriptors(mol)
212: AttributeError: module 'rdkit.Chem.Descriptors' has no attribute 'CalcMolDescriptors'
212:
212: ----------------------------------------------------------------------
212: Ran 15 tests in 34.707s
212:
212: FAILED (errors=1)
212: [20:38:53] WARNING: Omitted undefined stereo
212:
212: [20:38:53] WARNING: Proton(s) added/removed
212:
212: .......
212: ----------------------------------------------------------------------
212: Ran 7 tests in 125.984s
212:
212: OK
212:
212: InChI write Summary: 1162 identical, 0 suffix variance, 19 reasonable
212:
212: InChI read Summary: 685 identical, 0 variance, 496 reasonable variance
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 22.631s
212:
212: OK
212: ......
212: ----------------------------------------------------------------------
212: Ran 6 tests in 6.663s
212:
212: OK
212: .......<doctest rdkit.Chem.PandasTools[5]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
212: antibiotics = antibiotics.append({'Smiles':'CC1(C(N2C(S1)C(C2=O)NC(=O)CC3=CC=CC=C3)C(=O)O)C',
212: <doctest rdkit.Chem.PandasTools[6]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
212: antibiotics = antibiotics.append({
212: <doctest rdkit.Chem.PandasTools[7]>:1: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
212: antibiotics = antibiotics.append({
212: .................E..
212: ======================================================================
212: ERROR: test_write_V3000_to_sdf (main.TestWriteSDF)
212: ----------------------------------------------------------------------
212: Traceback (most recent call last):
212: File "/home/farah/rdkit/rdkit/Chem/UnitTestPandasTools.py", line 351, in test_write_V3000_to_sdf
212: PandasTools.WriteSDF(self.df, filename, forceV3000=True)
212: TypeError: WriteSDF() got an unexpected keyword argument 'forceV3000'
212:
212: ----------------------------------------------------------------------
212: Ran 27 tests in 27.735s
212:
212: FAILED (errors=1)
212: ............./home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BRICS.py:291: DeprecationWarning: The random parameter to shuffle() has been deprecated
212: since Python 3.9 and will be removed in a subsequent version.
212: random.shuffle(indices, random=random.random)
212: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/BRICS.py:299: DeprecationWarning: The random parameter to shuffle() has been deprecated
212: since Python 3.9 and will be removed in a subsequent version.
212: random.shuffle(compats, random=random.random)
212: .[20:44:08] WARNING: More than one matching pattern found - picking one
212:
212: [20:44:08] WARNING: More than one matching pattern found - picking one
212:
212: ..[20:44:10] Molecule does not have explicit Hs. Consider calling AddHs()
212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs()
212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs()
212: [20:44:10] Molecule does not have explicit Hs. Consider calling AddHs()
212: .........
212: ----------------------------------------------------------------------
212: Ran 25 tests in 111.015s
212:
212: OK
212: ..
212: ----------------------------------------------------------------------
212: Ran 2 tests in 1.228s
212:
212: OK
212: ..s...
212: ----------------------------------------------------------------------
212: Ran 6 tests in 9.538s
212:
212: OK (skipped=1)
212: **********************************************************************
212: File "/home/farah/rdkit/rdkit/Chem/BRICS.py", line 255, in main.FindBRICSBonds
212: Failed example:
212: res = list(FindBRICSBonds(m,randomizeOrder=True))
212: Exception raised:
212: Traceback (most recent call last):
212: File "/home/farah/anaconda3/lib/python3.9/doctest.py", line 1334, in __run
212: exec(compile(example.source, filename, "single",
212: File "<doctest main.FindBRICSBonds[8]>", line 1, in
212: res = list(FindBRICSBonds(m,randomizeOrder=True))
212: File "/home/farah/rdkit/rdkit/Chem/BRICS.py", line 290, in FindBRICSBonds
212: random.shuffle(indices, random=random.random)
212: AttributeError: module 'rdkit.RDRandom' has no attribute 'shuffle'
212: **********************************************************************
212: 1 items had failures:
212: 1 of 20 in main.FindBRICSBonds
212: Test Failed 1 failures.
212: ..[20:46:37] WARNING: not removing hydrogen atom without neighbors
212: .[20:46:37] WARNING: not removing hydrogen atom without neighbors
212: .[20:46:38] WARNING: no name column found on line 1
212: [20:46:38] WARNING: no name column found on line 2
212: [20:46:38] WARNING: no name column found on line 3
212: [20:46:38] WARNING: no name column found on line 4
212: [20:46:38] WARNING: no name column found on line 5
212: [20:46:38] WARNING: no name column found on line 6
212: [20:46:38] WARNING: no name column found on line 7
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212: [20:46:38] WARNING: no name column found on line 133
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212: [20:46:38] WARNING: no name column found on line 171
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212: [20:46:38] WARNING: no name column found on line 186
212: [20:46:38] WARNING: no name column found on line 187
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212: [20:46:38] WARNING: no name column found on line 189
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212: [20:46:38] WARNING: no name column found on line 191
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212: [20:46:38] WARNING: no name column found on line 193
212: [20:46:38] WARNING: no name column found on line 194
212: [20:46:38] WARNING: no name column found on line 195
212: [20:46:38] WARNING: no name column found on line 196
212: [20:46:38] WARNING: no name column found on line 197
212: [20:46:38] WARNING: no name column found on line 198
212: [20:46:38] WARNING: no name column found on line 199
212: [20:46:38] WARNING: no name column found on line 200
212: [20:46:38] WARNING: no name column found on line 201
212: [20:46:38] WARNING: no name column found on line 202
212: [20:46:38] WARNING: no name column found on line 203
212: [20:46:38] WARNING: no name column found on line 204
212: [20:46:38] WARNING: no name column found on line 205
212: [20:46:38] WARNING: no name column found on line 206
212: [20:46:38] WARNING: no name column found on line 207
212: [20:46:38] WARNING: no name column found on line 208
212: [20:46:38] WARNING: no name column found on line 209
212: [20:46:38] WARNING: no name column found on line 210
212: [20:46:38] WARNING: no name column found on line 211
212: [20:46:38] WARNING: no name column found on line 212
212: [20:46:38] WARNING: no name column found on line 213
212: [20:46:38] WARNING: no name column found on line 214
212: [20:46:38] WARNING: no name column found on line 215
212: [20:46:38] WARNING: no name column found on line 216
212: ......
212: ----------------------------------------------------------------------
212: Ran 10 tests in 2.664s
212:
212: OK
212: ..................
212: ----------------------------------------------------------------------
212: Ran 18 tests in 11.089s
212:
212: OK
212: ...
212: ----------------------------------------------------------------------
212: Ran 3 tests in 1.257s
212:
212: OK
212: ........
212: ----------------------------------------------------------------------
212: Ran 8 tests in 0.368s
212:
212: OK
212: ..
212: ----------------------------------------------------------------------
212: Ran 2 tests in 0.295s
212:
212: OK
212: ..
212: ----------------------------------------------------------------------
212: Ran 2 tests in 0.294s
212:
212: OK
212: .
212: ----------------------------------------------------------------------
212: Ran 1 test in 0.890s
212:
212: OK
212: ........
212: ----------------------------------------------------------------------
212: Ran 8 tests in 0.014s
212:
212: OK
212: ...
212: ----------------------------------------------------------------------
212: Ran 3 tests in 0.025s
212:
212: OK
212: ...
212: ----------------------------------------------------------------------
212: Ran 3 tests in 0.022s
212:
212: OK
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 0.028s
212:
212: OK
212: .......
212: ----------------------------------------------------------------------
212: Ran 7 tests in 0.270s
212:
212: OK
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 0.313s
212:
212: OK
212: ....
212: ----------------------------------------------------------------------
212: Ran 4 tests in 51.958s
212:
212: OK
212: ..........
212: ----------------------------------------------------------------------
212: Ran 10 tests in 1.153s
212:
212: OK
212: .
212: ----------------------------------------------------------------------
212: Ran 1 test in 0.012s
212:
212: OK
212: ..........
212: ----------------------------------------------------------------------
212: Ran 10 tests in 0.081s
212:
212: OK
212: ..../home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/Randomize.py:29: DeprecationWarning: The random parameter to shuffle() has been deprecated
212: since Python 3.9 and will be removed in a subsequent version.
212: random.shuffle(order, random=random.random)
212: .
212: ----------------------------------------------------------------------
212: Ran 5 tests in 1.876s
212:
212: OK
212: ................[20:50:30] Molecule does not have explicit Hs. Consider calling AddHs()
212: [20:50:30] Molecule does not have explicit Hs. Consider calling AddHs()
212: .....
212: ----------------------------------------------------------------------
212: Ran 21 tests in 83.367s
212:
212: OK
212: mol_197
212: 219.10,35.89,110.98,11.56,110.32,11.04,95.23,10.25,0.00
212: mol_223
212: 243.69,7.30,134.82,1.04,134.75,1.04,85.57,0.33,0.00
212: mol_269
212: 216.26,5.67,105.00,0.87,103.81,0.89,89.27,0.92,6.00
212: .
212: ----------------------------------------------------------------------
212: Ran 1 test in 0.005s
212:
212: OK
212: ...[20:50:36]
212:
212: ****
212: Pre-condition Violation
212: molecule has no conformers
212: Violation occurred on line 37 in file /project/build/temp.linux-x86_64-cpython-39/rdkit/Code/GraphMol/MolChemicalFeatures/MolChemicalFeature.cpp
212: Failed Expression: dp_mol->getNumConformers()
212: ****
212:
212: .
212: ----------------------------------------------------------------------
212: Ran 4 tests in 0.406s
212:
212: OK
1/1 Test facebook/mvfst#212: pythonTestDirChem ................***Timeout 1500.17 sec

0% tests passed, 1 tests failed out of 1

Total Test time (real) = 1500.47 sec

The following tests FAILED:
212 - pythonTestDirChem (Timeout)

Help me in removing these failures

[greglandrum]

@Rumeza this looks like you are mixing RDKit versions. The error messages reference code from what looks like a local github checkout: "/home/farah/rdkit/rdkit/Chem/BRICS.py" as well as what looks like a conda install: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/Randomize.py.
This is not going to work since the code you checked out from git doesn't match the code from a conda install.

What are you trying to do?

[Rumeza]

I have updated the enviornment variable and remove other enviornments. i am also facing error in building make from source code.

[ 43%] Building CXX object Code/GraphMol/Descriptors/CMakeFiles/Descriptors.dir/RDF.cpp.o

In file included from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/memory:63,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:2,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/char_traits.h:39,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/string:40,

             from /home/farah/rdkit/Code/RDGeneral/Invariant.h:17,

             from /home/farah/rdkit/Code/GraphMol/RDKitBase.h:21,

             from /home/farah/rdkit/Code/GraphMol/Descriptors/RDF.cpp:34:

In static member function 'static _Tp* std::__copy_move<_IsMove, true, std::random_access_iterator_tag>::__copy_m(const _Tp*, const _Tp*, _Tp*) [with _Tp = double; bool _IsMove = false]',

inlined from '_OI std::__copy_move_a2(_II, _II, _OI) [with bool _IsMove = false; _II = double*; _OI = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:497:30,

inlined from '_OI std::__copy_move_a1(_II, _II, _OI) [with bool _IsMove = false; _II = double*; _OI = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:524:42,

inlined from '_OI std::__copy_move_a(_II, _II, _OI) [with bool _IsMove = false; _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:531:31,

inlined from '_OI std::copy(_II, _II, _OI) [with _II = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _OI = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:622:7,

inlined from 'static _ForwardIterator std::__uninitialized_copy<true>::__uninit_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _ForwardIterator = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_uninitialized.h:110:27,

inlined from '_ForwardIterator std::uninitialized_copy(_InputIterator, _InputIterator, _ForwardIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _ForwardIterator = double*]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_uninitialized.h:151:15,

inlined from '_ForwardIterator std::__uninitialized_copy_a(_InputIterator, _InputIterator, _ForwardIterator, std::allocator<_Tp>&) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _ForwardIterator = double*; _Tp = double]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_uninitialized.h:333:37,

inlined from 'void std::vector<_Tp, _Alloc>::_M_range_insert(std::vector<_Tp, _Alloc>::iterator, _ForwardIterator, _ForwardIterator, std::forward_iterator_tag) [with _ForwardIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/vector.tcc:751:34,

inlined from 'void std::vector<_Tp, _Alloc>::_M_insert_dispatch(std::vector<_Tp, _Alloc>::iterator, _InputIterator, _InputIterator, std::__false_type) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; _Tp = double; _Alloc = std::allocator<double>]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_vector.h:1665:19,

inlined from 'std::vector<_Tp, _Alloc>::iterator std::vector<_Tp, _Alloc>::insert(std::vector<_Tp, _Alloc>::const_iterator, _InputIterator, _InputIterator) [with _InputIterator = __gnu_cxx::__normal_iterator<double*, std::vector<double> >; <template-parameter-2-2> = void; _Tp = double; _Alloc = std::allocator<double>]' at /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_vector.h:1383:22,

inlined from 'void RDKit::Descriptors::{anonymous}::getRDFDesc(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector<double>&)' at /home/farah/rdkit/Code/GraphMol/Descriptors/RDF.cpp:115:12,

inlined from 'void RDKit::Descriptors::{anonymous}::GetRDF(double*, const RDKit::ROMol&, const RDKit::Conformer&, std::vector<double>&)' at /home/farah/rdkit/Code/GraphMol/Descriptors/RDF.cpp:151:13,

inlined from 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector<double>&, int, const string&)' at /home/farah/rdkit/Code/GraphMol/Descriptors/RDF.cpp:211:11:

/home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:433:25: warning: 'void* __builtin_memcpy(void*, const void*, long unsigned int)' writing 1 or more bytes into a region of size 0 overflows the destination [-Wstringop-overflow=]

433 | std::memmove(__result, __first, sizeof(_Tp) * _Num);

  |             ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In file included from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/x86_64-conda-linux-gnu/bits/c++allocator.h:33,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/allocator.h:46,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/memory:64,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/stl_algobase.h:2,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/bits/char_traits.h:39,

             from /home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/string:40,

             from /home/farah/rdkit/Code/RDGeneral/Invariant.h:17,

             from /home/farah/rdkit/Code/GraphMol/RDKitBase.h:21,

             from /home/farah/rdkit/Code/GraphMol/Descriptors/RDF.cpp:34:

/home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/ext/new_allocator.h: In function 'void RDKit::Descriptors::RDF(const RDKit::ROMol&, std::vector&, int, const string&)':

/home/farah/anaconda3/x86_64-conda-linux-gnu/include/c++/11.2.0/ext/new_allocator.h:129:48: note: at offset 240 into destination object of size 240 allocated by 'operator new'

129 | return static_cast<_Tp*>(::operator new(__n * sizeof(_Tp)));

  |                                  ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~

[greglandrum]

@Rumeza that looks like a warning, not an error.
Please capture the complete output of running make install in a text file and then attach that text file to a message here (do not paste the full contents into a message... that's just not readable)

[Rumeza]

After updating i found these failures and warning during ctest
96% tests passed, 8 tests failed out of 212
34 - graphmoltestPickler (Subprocess aborted)
56 - smaTest1 (Subprocess aborted)
76 - testReaction (Subprocess aborted)
78 - testEnumeration (Subprocess aborted)
79 - rxnTestCatch (Failed)
80 - pyChemReactions (Failed)
81 - pyChemReactionEnumerations (Failed)
82 - pyChemReactionSanitize (Failed)
i also received some warning during make. all the details are mentioned in file attached.
waiting for your response

rdkit ctest failed.docx

[greglandrum]

@Rumeza : I don't have a straightforward way to read MS Word files on my linux machine. Please provide a text file.

[Rumeza]

See this file. Is it readable for you now?
rdkit-ctest-failed.txt

[greglandrum]

Yep. That's great.
Do you have the environment variable RDBASE set?

[Rumeza]

Thank you sir, Yes sir I have set enviornment variable for RDBASE.
These are all commands I have run so far
conda install -y cmake cairo pillow eigen pkg-config
conda install -y boost-cpp boost py-boost
conda install -y gxx_linux-64
conda install -c anaconda git.
git clone https://github.com/rdkit/rdkit.git
cd rdkit
mkdir build && cd build
cmake -DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_CPP_TESTS=ON -DPYTHON_NUMPY_INCLUDE_PATH="$(python -c 'import numpy ; print(numpy.get_include())')" -DBOOST_ROOT="$CONDA_PREFIX" ..
make
make install
export RDBASE=/home/farah/rdkit
export LD_LIBRARY_PATH=/home/farah/rdkit/lib:$LD_LIBRARY_PATH
export PYTHONPATH=/home/farah/rdkit:$PYTHONPATH
ctest

[Rumeza]

Can you guide me to pass the failed and Subprocess aborted test?

[greglandrum]

The output you shared does not correspond to the commands shown above and is not complete.
Please share all of the output, including the exact commands you ran, starting from running cmake, then running make install, then running ctest. Again, please put this in a plain text file.

[Rumeza]

Here is the complete output from cmake-make-make install-ctest and also ctest -V for failures output details
Ctest Failures- Discussion#1631.txt

[Rumeza]

Sir, can you help me in removing errors mentioned in my previously uploaded document?

…

On Tue, Mar 7, 2023, 10:34 Greg Landrum ***@***.***> wrote: The output you shared does not correspond to the commands shown above and is not complete. Please share *all* of the output, including the exact commands you ran, starting from running cmake, then running make install, then running ctest. Again, please put this in a plain text file. — Reply to this email directly, view it on GitHub <#6131 (reply in thread)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5TD4CIZLRBCSBJJH7UDXOTW23CFLANCNFSM6AAAAAAVHIGP34> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Rumeza]

Hi Sir, Can you help me in resolving failures in my rdkit ctest files? I have already uploaded errors file.

…

On Mon, Feb 27, 2023, 10:27 Greg Landrum ***@***.***> wrote: @Rumeza <https://github.com/Rumeza> this looks like you are mixing RDKit versions. The error messages reference code from what looks like a local github checkout: "/home/farah/rdkit/rdkit/Chem/BRICS.py" as well as what looks like a conda install: /home/farah/anaconda3/lib/python3.9/site-packages/rdkit/Chem/Randomize.py. This is not going to work since the code you checked out from git doesn't match the code from a conda install. What are you trying to do? — Reply to this email directly, view it on GitHub <#6131 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A5TD4COFDYSIJARLAM2XYU3WZQ3MXANCNFSM6AAAAAAVHIGP34> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[Rumeza]

The following tests FAILED:
34 - graphmoltestPickler (Subprocess aborted)
56 - smaTest1 (Subprocess aborted)
76 - testReaction (Subprocess aborted)
78 - testEnumeration (Subprocess aborted)
79 - rxnTestCatch (Failed)
80 - pyChemReactions (Failed)
81 - pyChemReactionEnumerations (Failed)
82 - pyChemReactionSanitize (Failed)

while running Ctest these tests failed
due to which i am unable to use rdkit.Chem. I have attached the complete file of commands i used to built rdkit and the failures and details of failures. As i am unable to locate the error and don't know how to make corrections in my C++ files to resolve these issues I need your guidence.

The files are attached here:
ctest output file after ctest -V command.txt
ctest failures detail.txt
ctest.txt
from make to PythonPath .txt
from cmake to cd rdkit.txt

RDKit version: 2022.09.5
OS: Ubuntu 20.04
Python version: Python 3.9.13
Are you using conda? No
If you are not using conda: how did you install the RDKit? I have built it using source code (github repository) mentioned in rdkit installation guide (https://www.rdkit.org/docs/Install.html)

I have used these commands to build my rdkit:
cmake -DPy_ENABLE_SHARED=1 -DRDK_INSTALL_INTREE=ON -DRDK_INSTALL_STATIC_LIBS=OFF -DRDK_BUILD_CPP_TESTS=ON -DPYTHON_NUMPY_INCLUDE_PATH="$(python -c 'import numpy ; print(numpy.get_include())')" -DBOOST_ROOT="$CONDA_PREFIX" ..
make
make install
export RDBASE=/home/farah/rdkit
export LD_LIBRARY_PATH=/home/farah/rdkit/lib:$LD_LIBRARY_PATH
export PYTHONPATH=/home/farah/rdkit:$PYTHONPATH
ctest